Gas-liquid and gas-liquid-solid catalysis in a mesh microreactor

A microstructured mesh contactor that can offer residence time of more than minutes is used for gas-liquid-solid hydrogenations and gas-liquid asymmetric hydrogenations. Applications for catalyst/chiral inductor screening and for kinetic data acquisition are demonstrated.     

Nuclear inelastic scattering spectroscopy of iron-sulfur cubane compounds

The potential of NIS spectroscopy to study the iron-sulfur clusters in metalloproteins is illustrated using model compounds. The origin of the intense low energy transfer bands is discussed.     

The synthesis of unsymmetrically N-substituted chiral 1,4,7-triazacyclononanes

A number of chiral unsymmetrically N-substituted 1,4,7-triazacyclononane ligands have been prepared by modular methods. The key step in the synthesis centres on the macrocyclisation of three tertiary amide precursors under standard Richman-Atkins conditions which allows for subsequent N-functionalisation.     

Metallation effects on the thermal interconversion of atropisomers of di(orthomethylarene)-substituted porphyrins

A new series of meso-substituted diaryl free-base and metalloporphyrins have been prepared. Each arene has been substituted with both a methyl group in the ortho position and a formyl group in the meta position. Rotation of the arene units is prevented at room temperature due to the steric restrictions imposed by the flanking methyl groups at the porphyrin beta-pyrrolic positions on the methyl groups at the ortho position on the meso-substituted arene unit. This allowed the alpha alpha and alpha beta atropisomers of this porphyrin to be separated and characterised. X-Ray crystallographic determination of the structure of the free-base porphyrin revealed a very flat porphyrin core. Metallation resulted in the isolation and characterisation of the nickel, zinc and copper derivatives. The assignments of the alpha alpha and alpha beta isomers are confirmed by X-ray crystallographic determination of the structures of the Cu(II) analogues. The copper alpha alpha structure exhibits a very twisted porphyrin core, the copper alpha beta structure is also distorted, but to a lesser degree. The activation energy for rotation has been calculated for each of the 2H, Ni and Zn derivatives. The energy required to rotate the arene ring increases in the order Ni < Zn approximately 2H. No significant difference in the free energy of rotation was observed between experiments carried out with the alpha alpha and small alpha beta isomers.     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

A model for describing the thermodynamics of multivalent host-guest interactions at interfaces

A model has been described for interpreting the binding of multivalent molecules to interface-immobilized monovalent receptors through multiple, independent interactions. It is based on the concept of effective concentration, C(eff), which has been developed before for multivalent binding in solution and which incorporates effects of lengths and flexibilities of linkers between interacting sites. The model assumes: (i). the interactions are independent, (ii). the maximum number of interactions, p(max), is known, (iii). C(eff) is estimated from (simple) molecular models. Simulations of the thermodynamics and kinetics of multivalent host-guest binding to interfaces have been discussed, and competition with a monovalent competitor in solution has been incorporated as well. The model was successfully used to describe the binding of a divalent guest to self-assembled monolayers of a cyclodextrin host. The adsorption data of more complex guest-functionalized dendrimers, for which p(max) was not known beforehand, was interpreted as well. Finally, it has been shown that the model can aid to deconvolute contributions of multivalency and cooperativity to stability enhancements observed for the adsorption of multivalent molecules to interfaces.     

Strong intramolecular secondary si.N bonds in trifluorosilylhydrazines

The simple silylhydrazines F(3)SiN(Me)NMe(2) (1), F(2)Si(N(Me)NMe(2))(2) (2), and F(3)SiN(SiMe(3))NMe(2) (3) have been prepared by reaction of SiF(4) with LiN(Me)NMe(2) and LiN(SiMe(3))NMe(2), while F(3)SiN(SnMe(3))NMe(2) (4) was prepared from SiF(4) and (Me(3)Sn)(2)NNMe(2) (5). The compounds were characterized by gas-phase IR and multinuclear NMR spectroscopy ((1)H, (13)C, (14/15)N, (19)F, (29)Si, (119)Sn), as well as by mass spectrometry. The crystal structures of compounds 1-5 were determined by X-ray crystallography. The structures of free molecules 1 and 3 were determined by gas-phase electron diffraction. The structures of 1, 2, and 4 were also determined by ab initio calculations at the MP2/6-311+G** level of theory. These structural studies constitute the first experimental proof for the presence of strong Si.N beta-donor-acceptor bonds between the SiF(3) and geminal NMe(2) groups in silylhydrazines. The strength of these non-classical Si.N interactions is strongly dependent on the nature of the substituent at the alpha-nitrogen atom of the SiNN unit, and has the order 3>4>1. The valence angles at these extremely deformed alpha-nitrogen atoms, and the Si.N distances are (crystal/gas): 1 104.2(1)/106.5(4) degrees, 2.438(1)/2.510(6) A; 3 83.6(1)/84.9(4) degrees, 2.102(1)/2.135(9) A; 4 89.6(1) degrees, 2.204(2) A.     

Characterization and genetic manipulation of peptide synthetases in Pseudomonas aeruginosa PAO1 in order to generate novel pyoverdines

PvdD, a nonribosomal peptide synthetase (NRPS) of Pseudomonas aeruginosa PAO1, incorporates two L-threonines into the siderophore pyoverdine. A pvdD mutant did not synthesize pyoverdine and lacked a high Mr iron-regulated cytoplasmic protein (IRCP). Analysis of other IRCPs and the P. aeruginosa genome enabled the remaining pyoverdine NRPSs to be identified. The pvdD mutation could be complemented in trans, enabling design of plasmid-based systems for the generation of novel pyoverdines. Introduction of a truncated pvdD gene resulted in attenuated forms of pyoverdine, and introduction of L-threonine-incorporating NRPSs from other organisms restored pyoverdine production to mutant cells. This is the first successful rational in vivo modification of NRPS modules outside of Bacillus subtilis. The systems employed did not allow incorporation of other residues into pyoverdine, indicating that there are multiple elements contributing toward substrate specificity in NRPSs.     

Rheology of binary colloidal structures assembled via specific biological cross-linking

The selectivity and range of energies offered by specific biological interactions serve as valuable tools for engineering the assembly of colloidal particles into novel materials. In this investigation, high affinity biological interactions between biotin-coated "A" particles (RA = 0.475 microm) and streptavidin-coated "B" particles (RB = 2.75 microm) drive the self-assembly of a series of binary colloidal structures, from colloidal micelles (a large B particle coated by smaller A particles) to elongated chain microstructures (alternating A and B particles), as the relative number of small (A) to large (B) particles (2 < or = NA/NB < or = 200) is decreased at a low total volume fraction (10(-4) < or = phiT < or = 10(-3)). At a significantly higher total volume fraction (phiT > or = 10(-1)) and a low number ratio (NA/NB = 2), the rheological behavior of volume-filling particle networks connected by streptavidin-biotin bonds is characterized. The apparent viscosity (eta) as a function of the shear rate gamma, measured for networks at phiT = 0.1 and 0.2, exhibits shear-rate-dependent flow behavior, and both the apparent viscosity and the extent of shear thinning increase upon an increase of a factor of 2 in the total volume fraction. Micrographs taken before and after shearing show a structural breakdown of the flocculated binary particle network into smaller flocs, and ultimately a fluidlike suspension, with increasing shear rate. Rheological measurements provide further proof that suspension microstructure is governed by specific biomolecular interactions, as control experiments in which the streptavidin molecules on particles were blocked displayed Newtonian flow behavior. This investigation represents the first attempt at measuring the rheology of colloidal suspensions where assembly is driven by biomolecular cross-linking.